I'd agree, it seems like the entirely wrong place to put a feature flag. Personally I'd go for either configuration file or database and then have a process for updating the feature flags.
The best implementation I've seen was in a Java project. Features where enable or disabled by either the properties file or the database. If a flag was set in the database, then that took precedence. New features would always be rolled out disabled in the properties file. Then in a controlled window the new features would be enabled for a few minutes and logs would be examined. If everything looked good the feature would then be enabled again. After a few days or weeks, the properties file would be updated to have the feature enabled by default and the flag in the database deleted in a later task.
The best implementation I've seen was in a Java project. Features where enable or disabled by either the properties file or the database. If a flag was set in the database, then that took precedence. New features would always be rolled out disabled in the properties file. Then in a controlled window the new features would be enabled for a few minutes and logs would be examined. If everything looked good the feature would then be enabled again. After a few days or weeks, the properties file would be updated to have the feature enabled by default and the flag in the database deleted in a later task.